Single mode (SM) fiber optical reader system and method for interrogating resonant waveguide-grating sensor(s)

ABSTRACT

An optical reader system is described herein which has a single mode (SM) optical fiber launch/receive system that uses one or more SM optical fibers to interrogate a biosensor and does not use multimode (MM) optical fibers to interrogate the biosensor. The use of the SM optical fiber launch/receive system effectively reduces angular sensitivity, reduces unwanted system reflections, improves overall angular tolerance, and improves resonant peak reflectivity and resonant peak width. Two specific embodiments of the SM optical fiber launch/receive system are described herein which include: (1) a dual fiber collimator launch/receive system; and (2) a single fiber launch/receive system that interrogates the biosensor at a normal incidence.

CROSS REFERENCE TO RELATED APPLICATION

This application is a divisional application of U.S. patent applicationSer. No. 11/058,155, filed Feb. 14, 2005 now U.S. Pat. No. 7,346,233.

BACKGROUND OF THE INVENTION

1. Field of the Invention

The present invention relates to a single mode (SM) fiber optical readersystem and method for interrogating a resonant waveguide grating (RWG)sensor to monitor biological events on top of the RWG sensor withoutsuffering from problems caused by parasitic reflections, whilepreserving wide angular tolerance and minimizing sensitivity to angularchanges.

2. Description of Related Art

Manufacturers of optical reader systems are always trying to design anew and improved optical reader system that can be used to interrogate abiosensor (e.g., RWG sensor, surface plasmon resonance (SPR) biosensor)to determine if a biomolecular binding event (e.g., biological bindingof ligands with analytes) occurred on a top surface of the biosensor.One such new and improved optical reader system is the subject of thepresent invention.

BRIEF DESCRIPTION OF THE INVENTION

The present invention includes an optical reader system which has asingle mode (SM) optical fiber launch/receive system that uses one ormore SM optical fibers to interrogate a biosensor and does not usemultimode (MM) optical fibers to interrogate the biosensor. The use ofthe SM optical fiber launch/receive system effectively reduces angularsensitivity, reduces unwanted system reflections, and improves resonantpeak reflectivity and resonant peak width. Two specific embodiments ofthe SM optical fiber launch/receive system are described herein whichinclude: (1) a dual fiber collimator launch/receive system; and (2) asingle fiber launch/receive system that interrogates the biosensor at anormal incidence.

BRIEF DESCRIPTION OF THE DRAWINGS

A more complete understanding of the present invention may be had byreference to the following detailed description when taken inconjunction with the accompanying drawings wherein:

FIG. 1 is a diagram showing an optical reader system which has a SMoptical fiber launch/receive system in accordance with the presentinvention;

FIG. 2 is a graph indicating an optical resonance from a RWG sensor;

FIG. 3 is a graph of power received vs. incident angle for a SMlaunch/SM receive fiber system and for a MM launch/SM receive fibersystem;

FIG. 4 is a graph of the spectrum of a superluminescent diode (SLD)reflection off a mirror observed with a entirely SM fiber path, and aspectrum observed when using a MM collection fiber;

FIG. 5 is a graph illustrating a resonance wavelength as a function oftime for a SM launch/SM receive fiber system compared with a MMlaunch/SM receive fiber system;

FIG. 6 is a graph illustrating a resonant wavelength vs. angle ofincidence for a MM launch/SM receive fiber system;

FIG. 7 are graphs illustrating a resonant wavelength vs. angle ofincidence for SM launch/SM receive fiber system measured with 8different collimators close to normal incidence;

FIG. 8 is a block diagram illustrating the basic components of a dualfiber collimator launch/receive system that is interrogating a RWGsensor in accordance with one embodiment of the present invention;

FIG. 9 is a graph illustrating a reflected spectrum from a RWG sensorusing the dual fiber collimator launch/receive system with and withoutcollimator “back-off”;

FIG. 10 is a graph illustrating a resonance intensity as a function ofcollimator back-off using the dual fiber collimator launch/receivesystem;

FIG. 11 is a graph illustrating a ratio of Fresnel reflection amplitudeto the peak power as a function of collimator back-off using the dualfiber collimator launch/receive system;

FIG. 12 is a graph illustrating a resonance full width at half maximumas a function of collimator back-off using the dual fiber collimatorlaunch/receive system;

FIG. 13 is a diagram illustrating the basic components of a single fiberlaunch/receive system that is interrogating a RWG sensor at a normalincidence in accordance with another embodiment of the presentinvention;

FIG. 14 is a 2D-plot illustrating the results of calculating theresonance intensity as a function of incident angle and wavelength for aRWG sensor;

FIG. 15 is a graph illustrating a peak resonance reflectivity as afunction of optical beam diameter for normal incidence illumination andoff-normal incidence illumination using a single fiber launch/receivesystem;

FIG. 16 is a graph illustrating a resonant peak full width half maximum(FWHM) as a function of beam diameter for normal incidence illuminationand off-normal incidence illumination using a single fiberlaunch/receive system;

FIG. 17 is a block diagram illustrating the basic components of a singlefiber collimator launch/receive system similar to the one shown in FIG.13 but this one also incorporates a circular polarizer (isolator) inaccordance with yet another embodiment of the present invention;

FIG. 18 is a graph illustrating a reflected spectrum from a RWG sensorinterrogated at normal incidence with and without the circular polarizer(isolator) in the single fiber launch/receive system;

FIGS. 19-28 are various graphs and charts indicating the results ofexperiments that were conducted to confirm some of the capabilities andfeatures of the single fiber launch/receive system.

DETAILED DESCRIPTION OF THE DRAWINGS

Referring to FIG. 1, there is a diagram that illustrates an opticalreader system 100 (interrogation system 100) which can interrogate oneor more RWG sensors 102 (one shown) to monitor biological events on topof the RWG sensor 102. The optical reader system 100 includes a lightsource 104 (e.g., SLD, laser), a launch/receive system 106 and a lightdetector 108 (e.g., photodiode, spectrograph, CCD camera). In accordancewith the present invention, the launch/receive system 106 utilizes SMoptical fiber 110 (plus other optics) to interrogate the RWG sensor 102and does not use any multimode (MM) optical fiber(s) to interrogate theRWG sensor 102. The advantages of using only SM optical fiber 110 withinthe launch/receive system 106 and two exemplary embodiments of the SMoptical fiber launch/receive system 106 are described in detail after abrief description is provided about the structure and functionality ofthe RWG sensor 102.

As shown in FIG. 1, the RWG biosensor 102 includes a thin (˜100 nm)layer of material 112 which is deposited on the surface of a diffractiongrating 114, forming a waveguide 116. The diffraction grating 114 istypically formed in a substrate material 118 by embossing, holography,or other methods. Alternatively, the diffraction grating 114 can beformed in the material 112 itself. Molecules 120 or bulk fluids (covermedium) may be deposited on a top surface 122 of the RWG sensor 102which alter the index of refraction at the top surface 122 of the RWGsensor 102. By probing the diffraction grating 114 with an optical beam124, one can detect this change (˜1 part per million) in the refractiveindex on the top surface 122 of the sensor 102. The top surface 122 ofthe RWG sensor 102 may also be coated with biochemical compounds (notshown) that only allow surface attachment of specific complementarymolecules 120, enabling the RWG sensor 102 to be both highly sensitiveand highly specific. Such RWG sensors 102 can be interrogated to detecta wide variety of chemical compounds or biomolecular binding events(e.g., binding of a drug to a protein) on the top surface 122. An arrayof RWG sensors 102 may be used in a microplate (for example) thatenables high throughput drug or chemical screening systems. For a moredetailed discussion about the structure and functionality of the RWGbiosensor 102 reference is made to the following document:

-   -   U.S. Pat. No. 4,815,843 entitled “Optical Sensor for Selective        Detection of Substances and/or for the Detection of Refractive        Index Changes in Gaseous, Liquid, Solid and Porous Samples”.        The contents of this document are incorporated by reference        herein.

One method that can be used to interrogate the RWG sensor 102 in orderto detect a biomolecular binding event is known as spectralinterrogation. Spectral interrogation entails illuminating the RWGsensor 102 with a multi-wavelength or broadband beam of light 124,collecting the reflected light 126, and analyzing the spectrum of thereflected light 126 with a spectral dispersing device such as aspectrometer 108. An example of a reflection spectrum from such a RWGsensor 102 is shown in FIG. 2. When biomolecular binding occurs at thesurface 122 of the RWG sensor 102, the resonance shifts slightly inwavelength, and it is this shift in the resonance wavelength that isdetected at the spectrometer 108. A second configuration that also usesspectral interrogation for interrogating the RWG sensor 102 entailsusing a tunable optical element such as laser (or Fabry-Perot filter, .. . ) as the source to modulate the wavelength of the input beam andthen the power reflected by the sensor is measured by a simple detector(e.g. photodiode, . . . ) to detect the resonance shifts.

It is well known that the use of fiber optics 110 is an efficient way ofinterrogating arrays of RWG sensors 102, because optical fiber 110 canbe used to easily route, split, and collect optical beams 124 and 126from arrays of RWG sensors 102. However, there are a number of importantaspects that need to be considered in order to create a robust andsensitive optical interrogation system 100 which utilizes optical fiber110. These aspects are described in detail below and include: (1)quality of spectrum; (2) angular sensitivity; and (3) angular tolerance.

Quality of Spectrum

For the spectral interrogation method, the quality of the spectrum inthe reflected light 126 is critically important. Ideally, the reflectedspectrum should contain only resonant reflected radiation, and should befree from Fresnel reflections that are caused by sensor interfaces, andother “parasitic” reflections within the optical path. These extraneousreflections distort the resonant peak shape, making it more difficult toaccurately locate the resonant peak. These extraneous reflections canalso make the optical system respond to resonant peak shifts in anon-linear manner. And, if these extraneous reflections change in time,they can cause extra noise or even false resonant peak shifts thatbehave like a binding event. To combat these problems, some havedesigned RWG sensors with multiple input and output gratings. Thesetypes of RWG sensors are described in the following documents:

-   -   M. Wiki, R. E. Kunz, G. Voirin, K. Tiefenthaler, and A. Bernard,        “Novel integrated optical sensor based on a grating coupler        triplet,” Biosensors and Bioelectronics 13 (1998) 1181-1185.    -   M. Wiki and R. E. Kunz, “Wavelength-interrogated optical sensor        for biochemical applications,” Optics Letters 25, No. 7, 463-465        (2000).    -   K. Cottier, M. Wiki, G. Voirin, H. Gao, and R. E. Kunz,        “Label-free highly sensitive detection of (small) molecules by        wavelength interrogation of integrated optical chips,” Sensors        and Actuators B 91 (2003) 241-251.        The contents of these documents are incorporated by reference        herein.

However, the designs of these types of RWG sensors are very complicated,and make the fabrication of the sensor itself more difficult. Thepresent invention can address this problem by using a SM optical fiberlaunch/receive system 106 which can create a high quality resonancespectrum without needing a complicated design of a RWG sensor 102.

Angular Sensitivity

An additional concern for the spectral interrogation method is thedependence of the resonant signal wavelength on the incident angle θ. Ifthe incident angle θ changes, then the resonant wavelength will shift.This can be seen from the approximate RWG resonant condition:

$\begin{matrix}{{\sin\;\theta} = {{\Lambda\; n_{eff}} - {\frac{\lambda}{\Lambda}.}}} & ( {{equation}\mspace{20mu} 1} )\end{matrix}$Here Λ is the pitch of the grating 114, θ is the angle of the incidentoptical beam 124, n_(eff) is the effective index of the waveguide 116,and λ is the wavelength of the resonance. One can then calculate,

$\begin{matrix}{{\frac{\mathbb{d}\lambda}{\mathbb{d}\theta} \approx {- \Lambda}},} & ( {{equation}\mspace{20mu} 2} )\end{matrix}$when the following approximation is made cos θ˜1 (small incident angle).For a grating pitch Λ of 500 nm this evaluates to 8.7 nm/deg or 500pm/mrad. This means that, if the global instrument accuracy target is,for example, in the range of 0.1 pm, then angular misalignments need tobe kept below two tenths of a microradian. Thus, in the absence of otherfiltering effects, such an interrogation system is highly sensitive tothe overall angular positioning of the RWG sensor 102. This sensitivityto angular positioning is particularly problematic if a microplateincorporating an array of RWG sensors 102 must be removed from thereading optics and reinserted during the course of an assay. A secondreason to decrease the angular sensitivity is that when one uses theinvention one frequently makes relative measurements by making acomparison between a “sample” signal and a “reference” signal. Inabsence of any filtering, this means that the angular stability betweenthe ‘reference’ optical path and the ‘sample’ optical path should remainstay stable within less than two tenths of a microradian. How the use ofexclusively SM optical fiber 110 within the launch/receive system 106reduces this angular sensitivity by orders of magnitude is describedbelow.Angular Tolerance

FIG. 3 shows an example of the angular tolerance of a multimode (100 μmcore) launch fiber/single mode (5.5 μm core) receive fiber and a singlemode (5.5 μm core) launch fiber/single mode (5.5 μm core) receive fiber.Here one can clearly observe the wider angular acceptance angle of themultimode fiber system. Since RWG sensors 102 may not be perfectly flat,or may be placed on the interrogation optics to within a range ofangles, one desires a fiber system with a wide collection angletolerance. This leaves a designer with two options in order to createwide angular tolerances use large core (multimode) fiber, or use shortfocal length lenses which necessitates interrogation of the sensor withsmall beam diameters.

As mentioned above, the use of SM fiber 110 is important for overallspectrum quality and stability of the optical signal. Due to the smallcore diameter of SM fiber 110, this forces the use of a short focallength lens to keep the angular tolerance as high as possible in orderto remain compatible with microplates having significant angulardeformation. However, the use of the short focal length lens produces asmall beam at the RWG sensor 102 which in turn causes an undesirablereduction in reflection efficiency and an undesirable increase inresonant spectral width. While one cannot eliminate these detrimentaleffects when using smaller beam sizes, the SM optical fiberlaunch/receive system 106 described below can, with the judicious use ofa normally incident SM optical fiber lens, improve the overall angulartolerance of the interrogation system 100, while minimizing the pricepaid in reflection efficiency and resonance spectral width.

SM Optical Fiber Launch/Receive System 106

A primary advantage of using only SM optical fiber 110 within thelaunch/receive system 106 is the elimination of multiple spatial modesin the fiber path. FIG. 4 shows the spectrum of a broadbandsuperluminescent diode (SLD) optical light source 104 that was obtainedwhen exclusively SM fiber, and SM fiber mixed with MM fiber was presentin the optical path. The high frequency structure present on thespectrum obtained with mixed SM/MM fiber is due to multipath (multiplespatial mode) interference effects. This high frequency structure on thespectrum can distort the shape of an optical resonance from the RWGsensor 102 and prevent accurate estimation of its wavelength. Shaking orotherwise mode-scrambling the multimode sections of the MM optical fibercan mitigate these effects, but not necessarily eliminate them. However,if all of the optical fiber in the launch/receive system 106 is SMoptical fiber 110 then these multimode effects can be eliminated for thesystem's band of operating wavelengths. A comparison of measurements ofthe resonance wavelength as a function of time, when observed with aSM/SM optical fiber launch/receive system 106 and a MM/SM optical fiberlaunch/receive system is shown in FIG. 5. It can be seen that theresonance wavelength is more stable for the exclusive SM optical fiberlaunch/receive system 106.

As described above, the range of collection angles that a lens, inconjunction with a small core diameter (e.g. single mode) fiber,collects is greatly reduced compared to a lens with a large core (e.g.multimode) fiber. While at first glance this reduced angular toleranceseems to make the SM optical fiber launch/receive system 106 lessdesirable, upon further inspection this reduced range of angles can beseen to be a distinct advantage for practical systems. As has also beendescribed above, the RWG sensor 102 will change resonant wavelength whentilted with respect to the input optical beam 124. However, when SMoptical fiber 110 is used on the receive end of the lens (collimator)this means that only a select angular band will be passed which in turnreduces the effects of these shifts in resonant wavelength.

Thus, when SM optical fiber 110 is used with the lens (collimator) thiseffectively creates a fiber/lens system that behaves as an “angularfilter” which can emit or receive rays of light 124 and 126 that arefrom a very narrow cone of angles. The approximate cone angle is givenby Δθ=d/f, (d=core diameter, f=focal length of lens) so that for examplewhen Corning FlexCor780 (5 μm core SM fiber) and an f=2 mm lens are usedthen Δθ˜2.5 mrad. A comparison of the angular sensitivity of a SMlaunch/SM receive system 106 and a MM launch/SM receive system is madein FIGS. 6 and 7. The MM launch/SM receive system has a dλ/dθ=7.5nm/deg, which is close to the 8.7 nm/deg mentioned above. Indeed, thisobserved value of 7.5 nm/deg (430 pm/mrad) can be more accuratelypredicted if dispersion effects of the waveguide are taken into account.However, for the SM launch/SM receive system 106, one observes awavelength sensitivity of only ˜0.18 nm/deg (10 pm/mrad). This SMangular sensitivity is almost two orders of magnitude less than the MMlaunch/SM receive system.

When modeling identical SM optical fiber 110 at the light emission andlight detection, it may be shown that the resonance wavelength is, inprinciple, insensitive to any angular misalignment of the RWG sensor 102because of this filtering effect. Indeed, it is only optical defects andaberrations that can create any residual wavelength change with angle.As such, to achieve angular sensitivities that are as low as possible,one should make the SM optical fiber launch/receive system 106 in amanner which takes into account the following parameters:

-   -   Optical quality: the aberration generated by the lens or by the        sensor surface deformation should be as low as possible.    -   Cleanliness: the optics and the sensor should be free of any        particle/dust.    -   It is important that the emission fiber and the detection fiber        are perfectly identical.    -   Any light propagating into the cladding of the SM optical fiber        110 should be removed.

In other words, any system effects that create a less than “ideal”optical path will create residual angular sensitivities for theinterrogation system 100. Even so, the practical angular sensitivity ofthe interrogation system 100 can easily be <10 pm/mRd. Such a lowwavelength shift with angle can make the removal/reinsertion of the RWGsensor(s) 102 during a biochemical test feasible, since small angularerrors will not significantly perturb the resulting signal.

Dual Fiber Launch/Receive System First Embodiment

Referring to FIG. 8, there is shown a dual fiber collimatorlaunch/receive system 106 a in accordance with one embodiment of thepresent invention. As described below, the dual fiber collimatorlaunch/receive system 106 a which is constructed with two SM opticalfibers 110 a and 110 b is an extremely advantageous tool forinterrogating a RWG sensor 102. By controlling the separation distanceor “back-off distance” of the collimator 902 from the biosensor 102, oneeffectively creates a separate input grating 114 a and an output grating114 b.

The separation of these input and output gratings 114 a and 114 bincreases as the collimator “back-off” distance is increased. The use ofseparate input and output gratings 114 a and 114 b allows one to rejectFresnel reflections and “parasitic” reflections caused by multiplereflections from various material interfaces in the RWG sensor 102.Fortunately, the reduction in Fresnel and parasitic reflection intensityis much greater than the reduction in resonance reflection intensity,because the resonance mode propagates through the waveguide 116 beforebeing coupled out. This guided mode decay is typically characterized bythe RWG sensor's leakage coefficient “alpha”, or α, where the intensityof the guided mode, I, as a function of position x is given by:I≈I₀e^(−αx).

Spectra obtained with and without collimator “back-off” are shown inFIG. 9. The progressive effect of the “back-off” distance upon theresonance and Fresnel reflection intensity are measurements displayed inFIGS. 10 and 11. The cost associated with backing off the fibercollimator 902 is a slow reduction in resonance signal amplitude. Thus,if the coupling loss coefficient, α, is carefully considered, one candesign the RWG sensor 102 for high resonance efficiency and very littleFresnel or parasitic reflection. In designing the RWG sensor 102 itshould be noted that the value of α effects the optimum collimatorstandoff distance. For example, this means that for an RWG sensor 102with a higher “alpha” one would operate the collimator 902 closer to theRWG sensor 102 than for a RWG sensor 102 with a lower “alpha”.

If one measures the amplitude of the resonant peak reflection as afunction of the “back-off” distance, then one may actually make ameasurement of this grating loss parameter, α. This is possible becauseof the fact that as the “back-off” distance increases the separationbetween the input and output areas of the grating 114 a and 114 b alsoincreases. Then, as long as the input and output gratings 114 a and 114b are completely separated, the returned resonant signal decaysexponentially in relation with the input/output separation distance.Such a measurement is useful for designing RWG sensors 102 and forperforming quality control of RWG sensor arrays.

An additional benefit of using the dual fiber collimator launch/receivesystem 106 a with “back-off” is that the resonance width decreases asthe “back-off” distance is increased. This width decrease is theconsequence of the fact that the beam is propagating over longerdistance inside the RWG. This is in fact one of the advantages of usinga continuous grating rather than the discrete gratings connected by awaveguide as described in the literature listed above. The narrower theresonance, the more accurately one can determine its position, for afixed signal-to-noise ratio. An example of this resonance narrowingeffect is shown in the measurements displayed in FIG. 12.

Single Fiber Launch/Receive System 106 b Second Embodiment

With the dual fiber collimator launch/receive system 106 a outlined inthe previous section, each SM fiber 110 a and 110 b is inherently offthe optical axis of the lens 902, so that interrogation is performed ata non-normal incident angle. At such a non-normal incident angle, it maybe shown that the peak reflectivity of the RWG sensor 102 rapidlydecreases when decreasing the beam diameter and, simultaneously, thespectral width of the resonance also increases. Both of these effectsnegatively impact the performance of the interrogation system 100.Smaller spot size is detrimental to the performance because theinterrogation system 100 interrogates a smaller region of the RWG sensor102 and as such becomes more sensitive to local perturbations andnon-uniformities. Increased resonant spectral width is also detrimental,because the ultimate resolution (in wavelength) of the interrogationsystem 100 increases with the resonance width and hence wider peaks leadto a degraded resolution.

On the other hand, a smaller spot size does have one significantpractical advantage. Real instruments have to deal with the non-flatnessof the microplates in which RWG sensors 102 are located. So, unless theinterrogation system 100 realigns the lenses 1402 (only one shown inFIG. 13) for every new measurement, the angular tolerance of theinterrogation system 100 has to be higher than the typical angulardeformations of the micoplate/RWG sensors 102. The angular tolerance isdirectly dictated by the beam diameter over the diffraction grating 114,the smaller diameters give better angular tolerances. That is, from thelimitations of diffraction, the angular acceptance of the interrogationsystem 100 is roughly dictated by the diffraction limit of the spot usedto interrogate the RWG sensor 102 as follows:

$\begin{matrix}{{\Delta\;\theta} \approx {\frac{\lambda}{d_{spot}}*0.5}} & ( {{equation}\mspace{20mu} 3} )\end{matrix}$where Δθ is the range of angles that may be collected, λ is thewavelength of the incident illumination 124, and d_(spot) is thediameter of the beam 124 at its focus on the RWG sensor 102. This allresults in a dilemma: one would like to use large spot sizes to get agood resonance definition and spatial averaging, but one would also liketo use small spot sizes to get a good angular tolerance.

The solution to this dilemma is to interrogate the RWG sensor 102 at anormal incidence. In this case, the single fiber launch/receive system106 b would use a single SM optical fiber 110 and one lens 1402 (seeFIG. 13) aligned with one another such that when the optical beam 124 isreflected by the RWG sensor 102, the reflected beam 126 comes back onitself and into the SM optical fiber 110. In this case, the SM opticalfiber 110 is used for both light injection and detection. The advantageof this configuration is that one can drastically decrease the diameterof the optical beam 124/126 over the RWG sensor 102 and keep excellentpeak reflectivity coefficients as well as resonance width. This isbecause the wavelength dependence of the resonance near normal incidenceis actually a parabolic function of angle, rather than the linearapproximation depicted in equation no. 1, which is valid at largerangles. A plot of this parabolic function of resonant reflectionefficiency as it relates to wavelength and angle for forward and reversepropagating modes in the RWG sensor 102 is shown in FIG. 14. In thisplot, the upper parabola represents the intensity of the forwardpropagating mode. And, the lower parabola represents the intensity ofthe reverse propagating waveguide mode. For a more detailed discussionabout this phenomenon, reference is made to the following documents:

-   -   F. Lemarchand, A. Sentenac, and H. Giovannini, “Increasing the        angular tolerance of resonant grating filters with doubly        periodic structures,” Opt. Lett. 23, No. 15, pp. 1149-1151        (1998).    -   F. Lemarchand, A. Sentenac, E. Cambril, and H. Giovannini,        “Study of the resonant behaviour of waveguide gratings:        increasing the angular tolerance of guided-mode filters,” J.        Opt. A: Pure Appl. Opt. 1 (1999), pp. 545-551.    -   D. Jacob, S. Dunn, and M. Moharam, “Normally incident resonant        grating reflection filters for efficient narrow-band spectral        filtering of finite beams,” J. Opt. Soc. Am. A 18, No. 9, pp.        2109-2120 (2001).        The contents of these documents are incorporated by reference        herein.

One can clearly see in FIG. 14 that near zero angle (normal incidence),the resonant wavelength changes only slowly with angle i.e dλ/dθapproaches zero. Using this information and equation no. 3, one mayobtain the graphs in FIGS. 15-16 which show the peak width calculated asa function of the beam diameter. As can be seen, one can considerablydecrease the beam diameter at normal incidence and still maintainresonance quality.

However, since there is no separation of the illumination and collectionregions as in the dual fiber collimator launch/receive system 106 a,interrogation at normal incidence with a single fiber launch/receivesystem 106 b suffers from the drawback that Fresnel and other parasiticreflections will be collected along with the resonant reflections.

To reduce or eliminate these reflections, one may add some form ofoptical isolator 1802 to the single fiber collimator launch/receivesystem 106 b as shown in FIG. 17. The optical isolator 1802 may beformed by placing a linear polarizer 1804 on top of the fiber lens 1402,and on top of the linear polarizer 1804 a quarter wave plate 1806 withits optical axis at 45° to the polarizer transmission axis may beplaced.

The spectral output of such an enhanced single fiber launch/receivesystem 106 b′ is shown in FIG. 18. These two additional components 1804and 1806 create the circular polarizer 1802 which rejects Fresnelreflections but allows resonant reflections to pass. The circularpolarizer 1802 causes all light 124/126 passing through it to becomecircularly polarized, and if the polarization is unchanged uponreflection as is the case with a Fresnel reflection, this same circularpolarization will be blocked when traveling back through the circularpolarizer 1802.

A detailed discussion is provided next to describe the optical modelthat was used to confirm some of the capabilities and features of thesingle fiber launch/receive system 106 b. In particular, the followingdiscussion describes the modeling and measurement of the resonance atnormal incidence when using the single fiber launch/receive system 106b.

1. Description of the Model at High Incidence Angle

A possible method for modeling finite size input beams 124 includesdecomposing the incident beam 124 into a sum of infinite plane waves andthen applying to each of those waves a reflection coefficient that wascalculated by using the RCWA modeling method. These equations are asfollows:

First, decompose the incident wave:

$\begin{matrix}{{{{Ei}(r)}:={\int{{{{FFPi}(k)} \cdot {\exp( {i \cdot k \cdot r} )}}{\mathbb{d}k}}}}{{{FFPi}(k)}:={{TF}( {{Ei}(x)} )}}{k:={2 \cdot \pi \cdot \frac{\sin(\theta)}{\lambda}}}} & (4.1)\end{matrix}$where:

-   -   Index i stands for ‘incident’.    -   FFP stands for far field pattern.    -   TF stands for Fourier transform.

Then, to calculate the energy distribution of the beam 126 reflected bythe grating 114, we apply the incident Far Field Pattern as a functionof a reflection coefficient which is a function of the wavelength λ andthe projection of the incident k vector along the grating vector asfollows in equation 4.2:

FFPr(k, λ) := FFPi(k, λ) ⋅ R(kx, λ) + r ⋅ FFPi(k, λ)${R( {{kx},\lambda} )}:=\frac{k\;{01 \cdot k}\; 10}{\alpha + {{i \cdot \Delta}\; k}}$${\Delta\; k}:={{\frac{2 \cdot \pi}{\lambda} \cdot ( {{- {neff}} + \frac{\lambda}{\Lambda}} )} + {k_{x}\mspace{31mu}({Forwardmode})}}$$\;{{\Delta\; k}:={{\frac{2 \cdot \pi}{\lambda} \cdot ( {{- {neff}} + \frac{\lambda}{\Lambda}} )} - {k_{x}\mspace{31mu}({Backwardmode})}}}$

After using the above equations to calculate the electric field of thereflected wave, the total amount of power collected, or effective totalreflectivity of the resonance from the sensor was determined bycalculating the cross integral product of this electric field with theelectric field output of the SM fiber 110.

This model can be applied to calculate, for instance, the resonanceshape as a function of the diameter of the input and output beams 124and 126. To help better explain what is happening, the plot in FIG. 19is used where the absolute value of the reflectivity is shown as afunction of the incidence angle (X-axis) and of the wavelength (Y axis).In this plot, the first approximation of the mode dispersion wasneglected and the leakage coefficient was assumed to be the same forbackward and forward propagating modes. This plot shows, for instance,that when one fixes an angle (on a vertical line) then one gets twosymmetric resonances corresponding to the backward and forwardpropagating modes. However, when one gets closer to the normalincidence, the backward and forward propagating modes are notindependent anymore and start interfering so that equation no. 4.2 is nolonger valid.

This plot can also be used to explain why the peak power of theresonance decreases and its width increases when using smaller beamdiameters. To explain this, we use one arm of the previous graph whichis shown in FIG. 20. First, consider an incident Gaussian beam which hasa diameter that corresponds to a given angular spread Δθ in the Fourierspace. Then, the smaller the beam size, the larger the angular spread.When increasing the angular spread, one can see on the graph that thisalso increases the wavelength spread because, for each incidence anglethere is a range of resonant wavelength. Thus, decreasing the beam sizeincreases the resonance width.

Additionally, consider only the central wavelength. If one draws ahorizontal line, only the incident angles that are close to the maximumof the resonance angle are reflected, the other angles are lost. So,when increasing the angular range, the percentage of light that isreflected decreases. Thus: decreasing the beam size decreases the peakpower of the resonance.

To illustrate these two basic rules, the following charts in FIGS. 21and 22 show the evolution of the resonance peak power and resonancewidth as a function of the diameter of the incident beam 124.

If we now calculate the coupling efficiency that we get in a SM/SMconfiguration, based on the previous equations, we get the followingresult:

This last equation shows that, when the sensor is angularly misaligned,the only thing that happens is that the amplitude of the resonancedecreases but neither the shape or the position of the resonance areaffected.2. Description of the Model at Normal Incidence2.1 Result of the Rigourous Coupled Wave Analysis (RCWA) Model

Because of interference effects between the backward and forwardpropagating modes near normal incidence, equation no. 4.2 that describesthe reflectivity versus the incident k vector and the wavelength is nolonger valid, and one must use the RCWA method to calculate the 2-Dreflectivity function.

The picture in FIG. 14 shows the reflectivity as a function of thewavelength (vertical axis) and the incident angle (horizontal axis)calculated with the RCWA method. As can be seen, each of the backward(lower curve) and forward (upper curve) resonance start being curvedwhen they come closer to normal incidence and both curves do not crosseach other at the center. As can also be seen, the forward propagatingmode disappears at the proximity of the normal incidence.

2.2 Experimental Evidence

To experimentally validate the reflectivity curve, we used a multimode(MM) fiber launch/single mode (SM) receive system at near normalincidence. This allowed one to vary the sensor angle over a wide rangewhile still collecting a substantial fraction of the reflected resonantlight. FIG. 23 are plots that show the evolution of the resonance as afunction of the tilt of the plate for an angle from −11 mRd to +11 mRd.As can be seen, when one comes close to the normal incidence, the peakpower of the forward resonance (peak on the left) decreases but remainsconstantly separated from the backward resonance by a finite amount(peak on the right). This result is in agreement with the prediction ofthe RCWA model. Next, we utilized the data of FIG. 23 to determine theirposition and peak power of the respective resonant peaks as shown inFIGS. 24 and 25. It should be appreciated that FIGS. 23 and 24 areresults of resonant wavelength and amplitude and resonant powerdistilled from the data shown in FIG. 22.

3. Advantage of Normal Incidence

One advantage of using normal incidence is to enable smaller incidentbeam diameters which make the interrogation system 100 less sensitive toangular misalignments. Referring back to the discussion of the peakresonance shape versus the beam diameter presented in section 1, if oneconsiders that the reflectivity is a parabolic curve, then it can beseen that the resonance enlargement due to an increase of the angularspread is much lower than in the case of the linear function shown inFIG. 26. On the other hand, if one utilizes a wavelength whichintersects the curve near the top of the hyperbole (near normalincidence), then one observes that a wider range of angles are reflectedefficiently for this wavelength than for wavelengths that intersect thecurve far away from normal incidence. Therefore, for interrogation nearnormal incidence, the amplitude of the reflected resonance will be leastaffected by an increase of the input beam angular spread. FIGS. 15 and16 show this evolution of the peak reflectivity and peak FWHM versus thebeam diameter calculated respectively at normal incidence and at highincidence angle. As can be seen, there is an advantage in using thenormal incidence configuration in terms of diffraction efficiency andwidth of the resonance, especially when decreasing the beam diameter.

4. Experimental Results at Normal Incidence

TABLE #1 summarizes the results obtained from a given RWG sensor wheninserting different lenses 1402 into the optical path to reduce the sizeof the beam 124.

TABLE #1 No lens No lens Focal 50 mm Focal 25 mm High Normal NormalNormal incidence incidence incidence incidence units Beam 0.5 0.5 0.10.052 mm diameter Measured 9.1 28.4 23 12 % reflectivity Peak ExpectedPeak 32 100 43 14 % reflectivity Measured 700 750 810 910 pm FWHMExpected 700 525 650 720 pm FWHM(*) Angular 1 1 3.4 7.1 mRdtolerance(**) (*)Calculated taking into account the spectrometerresponse. (**)Diameter of the angular tolerance corresponding to a 50%drop in power.

Although a non-negligible difference can be seen between the expectedvalues and the measured values which are probably due to gratingimperfections, the general conclusion is that one can reduce the beamdiameter by a factor of 10 without sacrificing much reflectionefficiency or increasing the resonance width appreciably.

5. Considerations when Utilizing a Small Beam at Normal Incidence

By using a focused beam at normal incidence, one may think that thedesign is similar to a MM configuration in that the input beam is notwell collimated. For instance, at first glance one may expect to get thesame huge sensitivity of 500 pm/mRd. However, by focusing the beam onthe RWG sensor, we image the Gaussian beam and we are then in an optimumSM configuration. So, as explained above, the optical models show thatthe SM launch/receive design is almost entirely insensitive to angularmisalignment (either off normal incidence or at normal incidence).

FIG. 27 shows several graphs where the angular sensitivity of theresonance position was measured at normal incidence with a beam diameterof 100 microns versus the tilt of the plate. As can be seen, thesensitivity is approximately 10 pm/mRd which is orders of magnitudebelow the sensitivity of the MM configuration.

A potential problem which may be caused by reducing the beam diameter isthat the measurement becomes more sensitive to local defects in thesensor. FIG. 28 is a graph that shows the change in resonance wavelengthas a function of the lateral motion of the sensor. As can be seen, thereare spectral shifts of up to 2 pm/micron everywhere and there are evensome local defects that where generated with up to 8 pm/microns.Likewise, another concern is that if there is a large non-homogeneity inthe amount of biochemical binding across the sensor, then the small beammay make the system more sensitive to these spatial variations,increasing the amount variation (or coefficient of variance, CV) in thebinding signal. However, judicious practices in the fabrication of thesensor itself, in the surface chemistry applied to the sensor, and inthe fluid handling used to introduce the biochemicals to the sensor, maybe used to mitigate these problems. Additionally, scanning of theoptical beam and spatial integration of the data over the sensor surfacemay be used to reduce the spatial sensitivities of small spotinterrogation. For example, refer to U.S. patent application Ser. No.11/027,547 entitled “Spatially Scanned Optical Reader System and Methodfor Using Same”. The contents of this document are incorporated byreference herein.

From the foregoing, it can be readily appreciated by those skilled inthe art that what has been described herein is a SM optical fiberlaunch/receive system 106 which uses one or more SM optical fibers 110to interrogate a biosensor 102 and does not use any MM optical fibers tointerrogate the biosensor 102. The use of the SM optical fiberlaunch/receive system 106 effectively reduces angular sensitivity,reduces unwanted system reflections, improves overall angular tolerance,and improves resonant peak reflectivity and resonant peak width. Also,described herein are two specific embodiments of the SM optical fiberlaunch/receive system 106 including: (1) a dual fiber collimatorlaunch/receive system 106 a; and (2) a single fiber launch/receivesystem 106 b that interrogates the biosensor 102 at a normal incidence.

Although several embodiments of the present invention have beenillustrated in the accompanying Drawings and described in the foregoingDetailed Description, it should be understood that the invention is notlimited to the embodiments disclosed, but is capable of numerousrearrangements, modifications and substitutions without departing fromthe spirit of the invention as set forth and defined by the followingclaims.

1. A system, comprising: a light source; a light detector; and a dualfiber collimator launch/receive system which includes: a first singlemode optical fiber to output a sensor input beam to a biosensor; and asecond single mode optical fiber to receive a sensor output beam fromthe biosensor, wherein said biosensor is a resonant waveguide gratingsensor.
 2. A system, comprising: a light source; a light detector; and adual fiber collimator launch/receive system which includes: a firstsingle mode optical fiber to output a sensor input beam to a biosensor;and a second single mode optical fiber to receive a sensor output beamfrom the biosensor, wherein said first and second single mode opticalfibers are physically separated from a lens located a predetermineddistance away from the biosensor which enables the rejection of Fresnelreflections and parasitic reflections which are created whileinterrogating the biosensor,
 3. A system, comprising: a light source; alight detector; and a dual fiber collimator launch/receive system whichincludes: a first single mode optical fiber to output a sensor inputbeam to a biosensor; and a second single mode optical fiber to receive asensor output beam from the biosensor, wherein said first and secondsingle mode optical fibers are physically separated from a lens locateda predetermined distance away from the biosensor that effectivelycreates an input grating and an output grating out of a single gratingwithin the biosensor while interrogating the biosensor.
 4. A system,comprising: a light source; a light detector; and a dual fibercollimator launch/receive system which includes: a first single modeoptical fiber to output a sensor input beam to a biosensor; and a secondsingle mode optical fiber to receive a sensor output beam from thebiosensor, wherein said first and second single mode optical fibers arephysically separated from a lens located an adjustable distance awayfrom the biosensor which enables one to measure a loss coefficient alphaα of the biosensor.
 5. A system, comprising: a light source; a lightdetector; and a dual fiber collimator launch/receive system whichincludes: a first single mode optical fiber to output a sensor inputbeam to a biosensor; and a second single mode optical fiber to receive asensor output beam from the biosensor, wherein the use of the first andsecond single mode optical fibers within said dual fiber collimatorlaunch/receive system eliminates undesirable spatial modes which wouldbe present if multimode optical fibers were used within said dual fibercollimator launch/receive system.
 6. A system, comprising: a lightsource; a light detector; and a dual fiber collimator launch/receivesystem which includes: a first single mode optical fiber to output asensor input beam to a biosensor; and a second single mode optical fiberto receive a sensor output beam from the biosensor, wherein the use ofthe first and second single mode optical fibers within said dual fibercollimator launch/receive system causes said dual fiber collimatorlaunch/receive system to have less sensitivity, in terms of wavelengthvariation, to angular deviations of the biosensor than if multimodeoptical fibers were used within said dual fiber collimatorlaunch/receive system.
 7. A system, comprising: a light source; a lightdetector; and a dual fiber collimator launch/receive system whichincludes: a first single mode optical fiber to output a sensor inputbeam to a biosensor; and a second single mode optical fiber to receive asensor output beam from the biosensor, wherein the use of the of thefirst and second single mode optical fibers within said dual fibercollimator launch/receive system causes a resonant wavelength associatedwith the biosensor to be more stable than if multimode optical fiberswere used within said dual fiber collimator launch/receive system.
 8. Amethod for interrogating a biosensor, said method comprising the stepsof: using a dual fiber collimator launch/receive system which does nothave multimode optical fibers incorporated therein to interrogate thebiosensor, wherein said dual fiber collimator launch/receive systemincludes: the first single mode optical fiber; the second single modeoptical fiber; and a lens, wherein said first single mode optical fiberis interfaced with a light source, wherein said first and second singlemode optical fibers are physically separated from said lens and saidlens is physically separated from said biosensor, wherein said firstsingle mode optical fiber emits a light beam generated by said lightsource such that the emitted light beam is passed through said lensbefore interfacing with the biosensor, wherein said biosensor reflectsthe light beam such that the reflected light beam passes through saidlens and said second single mode optical fiber and is received by alight detector, and wherein said biosensor is located within amicroplate; and moving said microplate and said biosensor relative tosaid dual fiber collimator launch/receive system which enables theemitted light beam to be scanned across different areas on saidbiosensor while interrogating said biosensor.
 9. The method of claim 8,wherein the use of the first and second single mode optical fiberswithin said dual fiber collimator launch/receive system eliminatesundesirable spatial modes which would be present if multimode opticalfibers were used within said dual fiber collimator launch/receivesystem.
 10. The method of claim 8, wherein the use of the first andsecond single mode optical fibers within said dual fiber collimatorlaunch/receive system causes said dual fiber collimator launch/receivesystem to have less sensitivity, in terms of wavelength variation, toangular deviations of the biosensor than if multimode optical fiberswere used within said dual fiber collimator launch/receive system. 11.The method of claim 8, wherein the use of the of the first and secondsingle mode optical fibers within said dual fiber collimatorlaunch/receive system causes a resonant wavelength associated with thebiosensor to be more stable than if multimode optical fibers were usedwithin said dual fiber collimator launch/receive system.
 12. The methodof claim 8, wherein said biosensor is a resonant waveguide gratingsensor.